A comparative survey of the anaerobic survival potential of four different bivalve species and the interference of associated bacteria has been carried out. Individuals from both subtidal and intertidal environments were considered by selecting the following species: Mytilus edulis (subtidal epifaunal), Spisula subtruncata (subtidal infaunal), Macoma balthica (intertidal infaunal) and Cerastoderma edule (intertidal infaunal). Anaerobiosis was simulated in the laboratory by subjecting individuals to the following conditions: nitrogen atmosphere, air atmosphere and anoxic seawater incubation. Moreover, the effect of the antibiotic CA (chloramphenicol) was investigated, either as a pre-treatment of individuals kept under normoxic conditions for a week or directly added to the anoxic incubation media. According to survival performances of the individuals, intertidal animals that use to cope with tidal fluctuations in the coastline (emersion processes) had an extraordinary greater capacity to survive aerial exposure as compared to both nitrogen gas and anoxic seawater incubations most likely due to their capacity to perform aerobiosis at certain rate from atmospheric oxygen availability. Specifically, Macoma balthica enlarged its survival potential up to 24.8 days (LT50) under air exposure at 12 °C as compared to other specific treatments used here (4.9 days). The latter pattern was also observed, although in a much lower magnitude, for the other intertidal species Cerastoderma edule that survived 3.7 and 4.6 days (LT50) under nitrogen atmosphere and anoxic seawater incubation, respectively as compared to 9.5 days for emersed individuals. In contrast to the subtidal species, aerial exposure of both intertidal species led to a much higher survival performances than incubation of individuals in anoxic media with the presence of antibiotic. Survival capacity of the subtidal species Mytilus edulis and Spisula subtruncata was statistically similar under air and nitrogen atmospheres and anoxic seawater incubation. Then, subtidal species have a limited ability to air breathing as a conclusion of a similar survival in atmospheric and anoxic seawater incubations. Remarkably, M. edulis represented the only exception when considering longer-term survival capacity compared to the LT50 values. Indeed, differences in LT90 values for M. edulis were statistically different, values decreasing significantly from 19.7–19.9 days (under both nitrogen and air atmospheres) to 16.7 days when individuals are incubated in anoxic seawater. This may be due to the adverse effects of anaerobic bacteria that spontaneously proliferate within the static seawater incubations. As well as for S. subtruncata, possible aerobic processes under aerial exposure of mussels seemed to be not significant for the enlargement of its survival potential, since results obtained for both air and nitrogen atmospheres are similar. Pre-treatment with the antibiotic chloramphenicol caused survival capacity to increase by a factor of approx. 2 (M. edulis) and 34–44% (S. subtruncata). In contrast to intertidal species, the direct addition of the antibiotic to the incubation media caused the highest survival performances in both subtidal species. Habitat differences and species-dependent variability must be considered as significant sources of variation when studying the anaerobic performance of individuals using the most common experimental anaerobic techniques to test survival potential.